How to use chemlambda for understanding DNA manipulations

UPDATE: Probably RNA better than DNA. The best entry point is that document. More in the references at the end of that doc. Or if you like just to see animations, there are aplenty (more than 350) in this collection.

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… or the converse: how to use DNA manipulations to understand chemlambda, this is a new thread starting with this post.

This is a very concrete, nice project, I already have some things written, but it is still in a very fluid form.

Everybody is invited to work with me on this. It would be very useful to collaborate with people which have knowledge about DNA and enzymes involved into the processes around DNA.

So, if you want to contribute, then you can do it in several ways:

by dedicating a bit of your brain power to concrete parts of this

by sending me links to articles which you have previously read and understood

by asking questions about concrete aspects of the project

by proposing alternative ideas, in a clear form

by criticizing the ideas from here.

I am not interested just to discuss about it, I want to do it.

Therefore, if you think that there is this other project which does this and that with DNA and computation, please don’t mention it here unless you have clear explanations about the connections with this project.

Don’t use authority arguments and name dropping, please.

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Now, if anybody is still interested to learn what is this about, after the frightening introduction, here is what I am thinking.

There is a full load of enzymes like this and that, which cut, link, copy, etc. strings of DNA. I want to develop a DNA-to-chemlambda dictionary which translates what happens in one world into the other.

This is rather easy to do. We need a translation of arrows and the four nodes from chemlambda into some DNA form.

Like this one, for example:

Then we need a translation of the chemlambda moves (or some version of those, see later) into processes involving DNA.

There is plenty of stuff in the DNA world to do the simple things from chemlambda. In turn, because chemlambda is universal, we get a very cheap way of defining DNA processes as computations.

Not as boolean logic computations. Forget about TRUE, FALSE and AND gates. Think about translating DNA processes into something like lambda calculus.

I know that there is plenty of research about using DNA for computation, and there is also plenty of research about relations between lambda calculus and chemistry.

But I am not after some overarching theory which comprises everything DNA, chemistry and lambda calculus.

Instead, I am after a very concrete look at tiny parts of the whole huge field, based on a specific formalism of chemlambda.

It will of course turn out that there are many articles relevant for what will be found here and there will be a lot of overlap with research already done.

Partially, this is one of the reasons I am searching collaborations around this, in order to not invent wheels all the time, due to my ignorance.